Magnesium in PDB 2h0x: Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme

The structure of Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme, PDB code: 2h0x was solved by D.J.Klein, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.30
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	180.599, 39.742, 70.669, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 23.4

The binding sites of Magnesium atom in the Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme (pdb code 2h0x). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme, PDB code: 2h0x:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:29.8 occ:1.00 O B:HOH261 2.1 19.2 1.0 O B:HOH288 2.1 25.6 1.0 O B:HOH289 2.1 27.4 1.0 OP2 B:C36 2.1 28.2 1.0 OP2 A:C2 2.2 26.0 1.0 OP2 B:G37 2.3 22.6 1.0 O3' B:A35 3.2 28.1 1.0 P B:C36 3.3 26.8 1.0 P B:G37 3.4 22.6 1.0 P A:C2 3.4 24.8 1.0 O3' A:G1 3.5 24.8 1.0 OP1 B:G37 3.7 22.4 1.0 O5' B:C36 4.1 27.3 1.0 O2' B:A35 4.2 29.4 1.0 C3' B:C36 4.2 22.7 1.0 C5' A:C2 4.2 27.2 1.0 O3' B:C36 4.3 23.2 1.0 O5' A:C2 4.3 25.6 1.0 OP1 B:C36 4.4 26.2 1.0 C3' B:A35 4.5 27.3 1.0 OP1 A:C2 4.5 25.5 1.0 O2' A:G1 4.5 27.0 1.0 O5' B:G37 4.6 22.4 1.0 C5' B:C36 4.7 24.5 1.0 C3' A:G1 4.9 25.0 1.0 C5' B:G37 4.9 23.3 1.0 C8 B:G37 4.9 21.8 1.0 C2' B:A35 4.9 27.7 1.0

Magnesium binding site 2 out of 6 in the Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:61.7 occ:1.00 N7 B:A110 2.4 22.2 1.0 O B:HOH235 2.5 29.8 1.0 O B:HOH374 2.7 38.7 1.0 O B:HOH266 2.8 32.6 1.0 C8 B:A110 3.2 22.3 1.0 OP2 B:A110 3.5 25.6 1.0 C5 B:A110 3.6 23.0 1.0 N4 B:C111 3.9 23.6 1.0 N6 B:A110 4.0 21.3 1.0 C5 B:C109 4.1 21.8 1.0 C6 B:A110 4.2 22.9 1.0 C6 B:C109 4.3 21.3 1.0 C5 B:C111 4.4 21.4 1.0 N9 B:A110 4.4 23.4 1.0 C4 B:C109 4.4 23.7 1.0 C4 B:C111 4.5 22.9 1.0 C4 B:A110 4.6 23.5 1.0 O5' B:A110 4.6 25.4 1.0 P B:A110 4.7 26.3 1.0 N1 B:C109 4.7 24.3 1.0 C3' B:C109 4.7 25.6 1.0 N3 B:C109 4.8 22.6 1.0 N4 B:C109 4.9 22.0 1.0 C2 B:C109 5.0 24.2 1.0

Magnesium binding site 3 out of 6 in the Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:26.9 occ:1.00 O2' B:U79 3.0 42.2 1.0 C2 B:U79 3.1 46.8 1.0 O B:HOH299 3.2 29.0 1.0 O2 B:U79 3.2 45.8 1.0 N4 B:C82 3.3 39.4 1.0 N1 B:U79 3.4 45.8 1.0 N3 B:U79 3.4 48.3 1.0 N4 B:C81 3.6 38.2 1.0 O B:HOH392 3.6 28.6 1.0 C2' B:U79 3.7 42.7 1.0 C5 B:C81 3.7 39.6 1.0 C4 B:C81 3.8 38.9 1.0 C1' B:U79 3.9 43.2 1.0 C6 B:U79 4.0 47.9 1.0 C5 B:C82 4.1 39.1 1.0 C4 B:U79 4.1 50.2 1.0 C4 B:C82 4.1 40.3 1.0 C5 B:U79 4.4 50.0 1.0 C6 B:C81 4.6 40.9 1.0 N3 B:C81 4.8 39.1 1.0 O4 B:U79 4.9 51.4 1.0 O4 B:U83 5.0 41.5 1.0

Magnesium binding site 4 out of 6 in the Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg504 b:27.6 occ:1.00 O2' B:A56 3.0 32.6 1.0 O B:HOH350 3.1 30.3 1.0 C4' B:C57 3.1 40.3 1.0 O B:HOH260 3.1 24.8 1.0 C5' B:C57 3.2 38.8 1.0 O B:HOH278 3.3 30.9 1.0 O4' B:C57 3.4 40.4 1.0 C6 B:U59 3.5 25.7 1.0 C2' B:U59 3.8 29.5 1.0 OP1 B:U59 3.8 30.3 1.0 C5 B:U59 3.8 23.6 1.0 N1 B:U59 3.9 26.6 1.0 C5' B:A58 4.0 33.5 1.0 C2' B:A56 4.1 31.5 1.0 C3' B:A58 4.1 31.3 1.0 O2' B:U59 4.2 32.0 1.0 O5' B:A58 4.3 38.9 1.0 O5' B:U59 4.3 29.2 1.0 C1' B:U59 4.4 28.1 1.0 P B:U59 4.5 30.0 1.0 C4' B:A58 4.5 32.8 1.0 O5' B:C57 4.6 35.4 1.0 C3' B:C57 4.6 41.0 1.0 O3' B:A58 4.6 29.4 1.0 C4 B:U59 4.6 22.9 1.0 C2 B:U59 4.7 25.6 1.0 C1' B:C57 4.8 40.7 1.0 O3' B:A56 4.9 33.6 1.0 N3 B:U59 4.9 24.3 1.0 C3' B:U59 5.0 29.6 1.0

Magnesium binding site 5 out of 6 in the Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg505 b:41.5 occ:1.00 O B:HOH333 2.0 36.5 1.0 O B:HOH331 2.0 29.2 1.0 O B:HOH332 2.0 39.5 1.0 O B:HOH211 2.1 36.0 1.0 O B:HOH330 2.1 32.5 1.0 O B:HOH300 2.3 44.0 1.0 O4 B:U100 3.6 50.9 1.0 O6 B:G102 4.1 41.8 1.0 O6 B:G101 4.2 40.6 1.0 OP2 B:A129 4.2 27.7 1.0 OP1 B:A129 4.2 27.4 1.0 N7 B:G101 4.3 47.1 1.0 C4 B:U100 4.3 51.1 1.0 O B:HOH340 4.3 36.0 1.0 C5 B:U100 4.4 50.2 1.0 N1 B:G102 4.7 40.4 1.0 C6 B:G102 4.7 43.1 1.0 O B:HOH341 4.7 45.8 1.0 P B:A129 4.7 27.8 1.0 O B:HOH210 4.9 42.8 1.0 C6 B:G101 4.9 43.1 1.0 C5 B:G101 5.0 45.2 1.0

Magnesium binding site 6 out of 6 in the Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Pre-Cleavage State of the Thermoanaerobacter Tengcongensis Glms Ribozyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg506 b:40.6 occ:1.00 O B:HOH399 2.3 47.0 1.0 O B:HOH400 2.6 49.9 1.0 O B:HOH378 3.1 39.7 1.0 N2 B:G122 3.4 18.3 1.0 O B:HOH322 4.3 34.1 1.0 C2 B:G122 4.4 20.5 1.0 N3 B:G122 4.4 19.1 1.0 C1' B:G123 4.5 25.9 1.0 C1' B:A110 4.5 24.2 1.0 O4' B:G123 4.6 26.1 1.0 O2' B:A110 4.7 22.6 1.0 O4' B:A110 4.8 24.3 1.0 O2' B:G123 4.8 27.1 1.0

D.J.Klein, A.R.Ferre-D'amare. Structural Basis of Glms Ribozyme Activation By Glucosamine-6-Phosphate Science V. 313 1752 2006.
ISSN: ISSN 0036-8075
PubMed: 16990543
DOI: 10.1126/SCIENCE.1129666